AMR/tests/testthat/test-pca.R

38 lines
2.0 KiB
R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("pca.R")
test_that("PCA works", {
library(dplyr)
resistance_data <- example_isolates %>%
filter(mo %in% as.mo(c("E. coli", "K. pneumoniae", "S. aureus"))) %>%
select(mo, AMC, CXM, CTX, TOB, TMP) %>%
group_by(order = mo_order(mo), # group on anything, like order
genus = mo_genus(mo)) %>% # and genus as we do here
summarise_if(is.rsi, resistance, minimum = 0)
expect_s3_class(pca(resistance_data), "prcomp")
expect_s3_class(prcomp(resistance_data), "prcomp")
ggplot_pca(pca(resistance_data), ellipse = TRUE)
})